Figure 3. Structural Features of the gp41CT_C Protein.

(A) The C^α positional RMSDs between the 20 low-energy structures of gp41CT_C are represented as a sausage plot of the representative gp41CT_C structure (line thickness is proportional to the RMSD values). The RMSDs from an average structure were calculated after aligning each α-helical segment separately. For residues located at the overlapping boundaries of individual segments, an average of the two RMSD values was calculated. Bending between the helical fragments is variable in the 20 calculated structures. (B) Cartoon representation of the gp41CT_C protein showing the extensive hydrophobic interface formed by Leu, Ile, Val, Ala, Trp and Phe residues (green sticks). (C) Surface representation of the gp41CT_C colored according to electrostatic surface potential. A basic patch is formed in the arginine-rich LLP1 motif. (D) Cartoon representation of the gp41CT_C protein showing Tyr and Trp residues as green sticks. Notice the cluster of six aromatic residues at the beginning of LLP3. The majority of aromatic residues are deeply buried in the interior of DPC micelle. (E) Surface representation of the gp41CT_C protein showing Arg and Lys residues (blue spheres).